Variant report

Variant	rs12739961
Chromosome Location	chr1:113996947-113996948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:109616898..109618683-chr1:113996110..113997630,2	MCF-7	breast:
2	chr1:113995710..113997522-chr1:113998226..113999728,2	MCF-7	breast:
3	chr1:113992312..113994525-chr1:113996440..113998587,2	K562	blood:
4	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232499	Chromatin interaction
ENSG00000197780	Chromatin interaction
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1106209	0.90[ASN][1000 genomes]
rs12071016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12132889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12354140	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354322	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1342650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1342652	0.92[MEX][hapmap]
rs17507114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1935747	0.92[MEX][hapmap]
rs2359412	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35724759	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6700878	0.95[ASN][1000 genomes]
rs7523209	0.90[ASN][1000 genomes]
rs7552618	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3444669	chr1:113995959-114038884	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12739961	AP4B1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113985000-113999000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:113994800-114004400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:113995400-113998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:113995400-113999000	Weak transcription	Stomach Mucosa	stomach
5	chr1:113995400-113999800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113995600-113999200	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:113995600-113999600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:113995600-114002400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:113995600-114003200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:113995800-113999200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:113996200-113997000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:113996400-113997800	Weak transcription	HUVEC	blood vessel
13	chr1:113996400-113999000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:113996400-113999000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:113996600-113997600	Weak transcription	A549	lung
16	chr1:113996600-113998200	Weak transcription	Hela-S3	cervix
17	chr1:113996600-113999000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:113996600-113999000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:113996600-113999000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:113996600-113999400	Weak transcription	Liver	Liver
21	chr1:113996600-114001200	Weak transcription	Small Intestine	intestine
22	chr1:113996600-114005800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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